Agroindustrial by-products from tomato, grape and myrtle given at low dosage to lactating dairy ewes: effects on rumen parameters and microbiota

Figures & data

Table 1. Effects of dietary treatments on rumen parameters.

	Diet^1				SEM	p-Value^2
	CON	EMB	TP	GM		D	S	D × S
pH	6.36^ab	6.40^ab	6.26^b	6.44^a	0.025	*	**	NS
Ammonia, mg/dL	8.44	10.65	9.19	7.52	0.522	NS	***	**
VFA^3, mol/100 mol
Acetate	62.54	60.72	66.23	59.20	1.044	NS	NS	NS
Propionate	17.28	17.51	18.19	16.60	0.459	NS	***	NS
Butyrate	14.55	13.05	14.54	13.54	0.443	NS	***	NS
Isovalerianic	0.29	0.30	0.29	0.24	0.014	NS	**	NS
Valerianic	8.32	8.29	5.88	5.33	0.707	NS	**	NS
Acetate:Propionate	3.75	3.61	3.68	3.60	0.064	NS	**	NS
Acetate, %	66.56	66.68	67.01	66.42	0.358	NS	***	NS
Propionate, %	18.28	19.14	18.39	18.65	0.342	NS	NS	NS
Butyrate, %	15.15	14.18	14.60	14.93	0.260	NS	***	NS
CH4emission^4,5	29.21	27.73	30.62	27.49	0.570	NS	NS	NS
CH4/kg of DM^5	17.36	18.23	20.28	17.40	0.476	NS	**	NS
CH4/kg of milk^5	35.00	34.95	37.77	27.77	1.565	NS	*	NS

^a,bMeans within a row with different superscripts are different (p < .05).

¹CON: control diet; EMB: diet containing 75 g/d per head of exhausted myrtle berries; TP: diet containing 100 g/d per head of tomato pomace; GM: diet containing 100 g/d per head of grape marc; ²D: effect of diet; S: effect of sampling time; NS indicates p > .10005; ³VFA: volatile fatty acids; ⁴Estimated according to Moss et al. (2000); ⁵CH₄: Methane, mol/mol of VFA.

*p < .05; **p < .01; ***p < .001.

Figure 1. Temporal evolution of rumen NH3 production during the trial.

Table 2. Diet’s effect on biodiversity indices of rumen microbial population.

Index	Sampling	Diet^1				SEM^2	AOV p-value^3
		CON	EMB	TP	GM		D	S	D × S
Shannon	1	2.48^ab	3.02^a	2.38^ab	2.23^b	0.06	**	NS	NS
	2	2.48	2.65	2.59	2.23	0.05
Simpson	1	0.76^ab	0.86^a	0.74^ab	0.71^b	0.01	*	NS	NS
	2	0.76	0.79	0.80	0.70	0.01

^a,bMeans within a row with different superscripts are different (p < .05).

¹CON: control diet; EMB: diet containing 75 g/d per head of exhausted myrtle berries; TP: diet containing 100 g/d per head of tomato pomace; GM: diet containing 100 g/d per head of grape marc; ²SEM: standard error of the mean; ³D: effect of diet; S: effect of sampling time; NS indicates p > .05.

*p < .05; **p < .01.

Figure 2. Violin plot of alpha diversity as measured with different metrics. Different colours indicate different diet treatments, violin shapes represent all possible results, with thickness indicating density. No significant differences at p < .01 were observed between groups.

Figure 3. Beta diversity. Non-metric multidimensional scaling (NMDS) based on Bray–Curtis dissimilarity matrix shows time as possible element of diversity between samples.

Table 3. Taxonomic identity of the rejected hypotheses in EMB vs CON Diet.

Counts	LogFC	p adjusted	Phylum	Class	Order	Family	Genus
57.06	1.10	.04	Bacteroidetes	Bacteroidia	Bacteroidales	Paraprevotellaceae	n.a
15.82	1.49	.05	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	n.a
278.96	1.56	.05	Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	n.a
5.59	2.02	.05	Cyanobacteria	Chloroplast	Streptophyta	n.a	n.a
12.65	1.80	.05	SR1	n.a	n.a	n.a	n.a
6.68	−1.14	.05	Firmicutes	Clostridia	Clostridiales	Veillonellaceae	Schwartzia
132.02	1.36	.14	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillospira
23.71	−0.88	.14	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Asteroleplasma
1.38	2.61	.14	Spirochaetes	Spirochaetes	Sphaerochaetales	Sphaerochaetaceae	Sphaerochaeta
1.86	2.26	.14	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	n.a

Top10 bacteria ranked by significance for DESeq2 results in EMB vs CON comparison.

FC: fold change; n.a.: not available.

Table 4. Taxonomic identity of the rejected hypotheses in GM vs CON Diet.

Counts	LogFC	p adjusted	Phylum	Class	Order	Family	Genus
14.59	2.28	.17	SR1	n.a	n.a	n.a	n.a
9.04	2.50	.41	Tenericutes	Mollicutes	Anaeroplasmatales	Anaeroplasmataceae	n.a
56.92	−1.81	.44	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	n.a
2.47	2.38	.60	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	n.a
12.55	−0.97	.66	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
76.95	0.74	.79	Fibrobacteres	Fibrobacteria	Fibrobacterales	Fibrobacteraceae	Fibrobacter
123.65	−0.39	.91	Firmicutes	Clostridia	Clostridiales	Veillonellaceae	Succiniclasticum
135.37	−0.46	.99	Firmicutes	Clostridia	Clostridiales
25.45	−1.31	.99	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
16.09	0.88	.99	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium

Top 10 bacteria ranked by significance for total DESeq2 results in GM vs CON comparison.

FC: fold change; n.a.: not available.

Table 5. Taxonomic identity of the rejected hypotheses in TP vs CON Diet.

Counts	LogFC	p adjusted	Phylum	Class	Order	Family	Genus
4.86	5.61	.00	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
56.03	−1.72	.13	Tenericutes	Mollicutes	Anaeroplasmatales	Anaeroplasmataceae	Anaeroplasma
63.51	1.05	.55	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
43.28	−0.82	.55	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus
27.11	−1.49	.55	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
17.16	1.73	.55	Bacteroidetes	Bacteroidia	Bacteroidales	Paraprevotellaceae	Prevotella
4.75	−1.08	.55	Synergistetes	Synergistia	Synergistales	Dethiosulfovibrionaceae	Pyramidobacter
4.57	−4.26	.55	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
38.46	−1.38	.86	Cyanobacteria	4C0d-2	YS2	n.a	n.a
22.00	0.99	.86	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium

Top 10 bacteria ranked by significance for total DESeq2 results in TP vs CON comparison.

FC: fold change; n.a.: not available.

Moss AR, Jouany JP, Newbold J. 2000. Methane production by ruminants: its contribution to global warming. Ann Zootech. 49(3):231–253.

 Google Scholar